irAEMM/README.md

Immunotherapy related adverse effects toolbox

Manage images and data related to irAE project.

Slicer module

A Slicer module was created to assist Radiology and Nuclear Medicine phsicians in reviewing the images. The following lists the installation, setup and usage of the module.

Installation

Here is the installation video that shows required steps.

Download the code and dependencies. Unzip. To have Slicer know where the files are, open Slicer, and under Edit->Application settings select Modules section. Under Paths, click on Add and navigate to newly unzipped directories. We need labkeyBrowser and DICOMtools from SlcierLabkeyExtension and slicerModule from iraeMM code. After clicking OK, Slicer will and has to be restarted.

Setup

To access LabKey, the Slicer tools must be configured. Do that by selecting LabKey->labkeyBrowser module from module list and fill appropriate fields.

Onko-nix

For accessing OIL internal site, the settings are:

• Server: `http://onko-nix.onko-i.si:8080
• Labkey username: username, given at the LabKey site, typically your email
• Labkey password: password, generated when accessing LabKey site

The rest needn't be changed.

Setup verification and storage

Once the data is entered, click on Init to check whether LabKey can be accessed. If the button turns green, you are OK. Do Save configuration.

Usage

See video of module use, illustrating steps below. Old version here.

Use Labkey->iraemmBrowser module. The Patients section lets you select the patient and corresponding visit. On Load the data gets loaded from the server.

Converting segmentations

The segmentations on server are stored as label maps, which have to be converted to segments for Slicer. To do that, select Segmentations module from the drop-down menu. Under Active segmentations, a new segmentation must be created by selecting Create new segmentation option from the pull down menu. Scroll down to Export/import models and labelmaps and change the mode to Import by moving the radio button selection. The Input type should be set to labelmap. Input node should match selected patient/visit pair and should end in Segm. Click on Import button further down.

Removing labelmap volume

The source labelmap volume will obscure other volumes, so we should delete it. Do that by selecting Volumes module and rotating˛Active volume to point to labelmap used in segmentation creation. Once selected, select Delete current volume from the same pull down menu next to Active volume.

Viewing segmentations

Labelmap was converted to a set of Segments, which are listed in the Segmentations module. By clicking on the open/closed eye icon, a segment can be made visible or invisible on the windows. Further setup can be made in the View controls module, where visibility and mode of each volume can be adjusted. For the segmentations, which appear in the top layer, either continuous, continuous with sharpened edges or edge only mode are available by clicking on display icon.

Entering review

The module has a review section. Select LabKey->iraemmBrowser and navigate to review secion. Four levels of agreement can be selected and an addition Comments field is available. Once filled, review is submitted by clicking on Submit button. Choices can be changed any time and new values can be pushed to database with further clicks of the button.

Clearing

Once done, a patient should be cleared to minimize interference in segmentation evaluation. Do that by pressing Clear in Patients section of the iraeMMBrowser module.

Dependencies

To access LabKey, the python API was used. Anonymization and NIfTI conversion are based on phenomenal nibabel tools. Data storage is provided by Orthanc with associated interface.

Usage

Anonymization must be run as a tomcat8 user for access to data files. Check setup in the anonymization.py and run it with runPython.sh anonymization.py.